We propose to organize a meeting titled Automated Function Prediction in the summer of 2011 (AFP 2011). The meeting will consist of two components, the first being a series of talks (invited and contributed) and discussion sections dedicated to protein function research, with an emphasis on the theory and practice of computational methods utilized in functional annotation. The second component will provide a large-scale assessment of computational methods through participation in the Critical Assessment of Functional Annotation (CAFA), an experiment based on a highly-regarded CASP assessment protocol for protein structure prediction. Understanding protein function is critical to understanding life at the molecular level. It also provides important insights into understanding disease since many conditions arise as a consequence of the loss, disruption or gain of protein function. However, the rapidly growing number of sequenced organisms poses a challenge for functional genomics projects because of the need to experimentally annotate known proteins. Therefore, protein function prediction research is important for biomedical research. AFP 2011 will stimulate discussion and the exchange of ideas/experience regarding functional ontologies, experiments leading to functional annotations, biases or limitations introduced in the process, methodologies for predicting function, and effectiveness of these algorithms. The AFP 2011 meeting will be associated with the 19th annual international conference on Intelligent Systems for Molecular Biology (ISMB), the official conference of the International Society for Computational Biology (ISCB). ISMB 2011 will be held in Vienna, Austria, in July of 2011, with AFP 2011 as a Special Interest Group meeting. This will not only ensure wide participation from the ISCB community, but also reduce costs compared to a stand-alone meeting. By organizing the CAFA experiment, we aim to not only assess the current methodology for function prediction, but also provide incentive for investigators to develop new and more accurate techniques that are necessary for the continuous progress of the field. The organizers of the meeting will strongly encourage broad participation of senior and junior scientists (including post-docs and students) as well as diversity. Collaboration is established with two universities recognized as Historically Black Colleges and Universities by the US Department of Education (Delaware State University and Jackson State University). Funding is requested for travel allowances only. PUBLIC HEALTH RELEVANCE: We propose to organize a meeting titled Automated Function Prediction in the summer of 2011 (AFP 2011). The meeting will consist of a series of talks and discussion sections dedicated to protein function research and will also provide a large-scale assessment of computational methods for automated functional annotation of proteins.